magnes::JEquation Class Reference

The base class for the computation of scalar coupling constants. More...

#include <jequation.h>

Inheritance diagram for magnes::JEquation:

Classes
class	Parameter
	Representation of a parameter in an empirical equation. More...
class	ParameterSet
	A set of parameters. More...

Public Member Functions
	JEquation ()
	Constructor.
virtual	~JEquation ()
	Virtual destructor.
virtual float	GetJ (const Frame &frame, size_t i, size_t j)=0
void	CoupledPairs (Molecule *molecule, std::vector< magnes::CouplingConstant > &pairs)
virtual std::string	Name () const =0
virtual std::pair< std::string, std::string >	CoupledNuclei () const =0
virtual int	NBonds () const =0
virtual std::string	Description () const
	html description of the equation This function should be overloaded in inheriting classes to provide a simple description of the equation in HTML format
std::string	Group () const
	The group to which the equation belongs This function is mainly use to group equations inside MagNes-JCoupling equation box according to the class of compounds they were designed for. returns "General" by default.
void	SetGroup (const std::string &group)
virtual bool	SelectFirstAtom (const Molecule *molecule, size_t i)=0
virtual bool	SelectSecondAtom (const Molecule *molecule, size_t i)=0
void	SetParameters (std::vector< Parameter > &newparams, int i)
const ParameterSet &	GetParameterSet (size_t i) const
ParameterSet &	GetParameterSet (size_t i)
const ParameterSet &	GetCurrentParameterSet () const
ParameterSet &	GetCurrentParameterSet ()
const std::vector< ParameterSet > &	GetParameterSets () const
std::vector< ParameterSet > &	GetParameterSets ()
size_t	GetCurrentParameterSetIndex () const
void	SetCurrentSet (size_t n)
virtual void	InitParameters ()=0
void	SaveParameters (std::ostream &s) const
void	LoadParameters (std::istream &s)

Protected Attributes
size_t	m_s1
size_t	m_s2

Detailed Description

The base class for the computation of scalar coupling constants.

JEquation is a base class for implementation of empirical equations for scalar J coupling computations using empirical equations, like Karplus Altona....

Member Function Documentation

CoupledNuclei()

virtual std::pair< std::string , std::string > magnes::JEquation::CoupledNuclei ( ) const

pure virtual

Returns

the names of two nuclei being coupled

Implemented in magnes::CCCHEquation, and magnes::HCCHEquation.

CoupledPairs()

void magnes::JEquation::CoupledPairs	(	Molecule *	molecule,
		std::vector< magnes::CouplingConstant > &	pairs
	)

Fill the vector

Parameters

pairs	with all computable J pairs in Molecule
molecule

GetCurrentParameterSet() [1/2]

const ParameterSet& magnes::JEquation::GetCurrentParameterSet

(

)

const

Returns

set of parameters currently active

GetCurrentParameterSet() [2/2]

ParameterSet& magnes::JEquation::GetCurrentParameterSet

(

)

Returns

set of parameters currently active

GetCurrentParameterSetIndex()

size_t magnes::JEquation::GetCurrentParameterSetIndex

(

)

const

Returns

the index of the active parameter set

GetJ()

virtual float magnes::JEquation::GetJ ( const Frame &  frame, size_t  i, size_t  j  )

pure virtual

Returns

the scalar coupling constant in Hz for atoms

Parameters

i	and
j	(from 0 to N-1) in corformer
frame

GetParameterSet() [1/2]

const ParameterSet& magnes::JEquation::GetParameterSet

(

size_t

i

)

const

Returns

a reference of the parameters at index

Parameters

i

GetParameterSet() [2/2]

ParameterSet& magnes::JEquation::GetParameterSet

(

size_t

i

)

Returns

a reference of the parameters at index

Parameters

i

GetParameterSets() [1/2]

const std::vector<ParameterSet>& magnes::JEquation::GetParameterSets

(

)

const

Returns

a const reference to a vector with all parameters sets

GetParameterSets() [2/2]

std::vector<ParameterSet>& magnes::JEquation::GetParameterSets

(

)

Returns

a non const reference to a vector with all parameters sets

InitParameters()

virtual void magnes::JEquation::InitParameters ( )

pure virtual

Init the parameter list

LoadParameters()

void magnes::JEquation::LoadParameters

(

std::istream &

s

)

Load parameters from stream

Name()

virtual std::string magnes::JEquation::Name ( ) const

pure virtual

Returns

the name of the equation to be displayed

NBonds()

virtual int magnes::JEquation::NBonds ( ) const

pure virtual

Returns

the number of bonds between the two coupled nuclei

Implemented in magnes::CCCHEquation, and magnes::HCCHEquation.

SaveParameters()

void magnes::JEquation::SaveParameters

(

std::ostream &

s

)

const

Save set of parameters to stream

SelectFirstAtom()

virtual bool magnes::JEquation::SelectFirstAtom ( const Molecule *  molecule, size_t  i  )

pure virtual

Check if atom

Parameters

i	can be selected

Implemented in magnes::CCCHEquation, and magnes::HCCHEquation.

SelectSecondAtom()

virtual bool magnes::JEquation::SelectSecondAtom ( const Molecule *  molecule, size_t  i  )

pure virtual

Check if the second atom

Parameters

j	can be selected

Implemented in magnes::CCCHEquation, and magnes::HCCHEquation.

SetCurrentSet()

void magnes::JEquation::SetCurrentSet

(

size_t

n

)

set the active parameter set to

Parameters

n

SetGroup()

void magnes::JEquation::SetGroup

(

const std::string &

group

)

set the group which the equation belongs

SetParameters()

void magnes::JEquation::SetParameters	(	std::vector< Parameter > &	newparams,
		int	i
	)

Fill the set of parameters sets to

Parameters

newparams	in position
i

Member Data Documentation

m_s1

size_t magnes::JEquation::m_s1

protected

first atom selected

m_s2

size_t magnes::JEquation::m_s2

protected

second atom selected

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The documentation for this class was generated from the following file:

• /Users/armando/worksrc/magnes-code/trunk/jcoupling/jequation/jequation.h